feat(silo): allow updating of string columns

[taepper]

resolves #1389

Summary

This adds the missing update method to the three types of string columns

PR Checklist

• All necessary documentation has been adapted or there is an issue to do so.
• The implemented feature is covered by an appropriate test.

[github-actions]

This is a preview of the changelog of the next release. If this branch is not up-to-date with the current main branch, the changelog may not be accurate. Rebase your branch on the main branch to get the most accurate changelog.

Note that this might contain changes that are on main, but not yet released.

Changelog:

0.13.0 (2026-07-28)

⚠ BREAKING CHANGES

• preprocessing: the database config options defaultNucleotideSequence and defaultAminoAcidSequence have been removed. sequenceName is now required on all nucleotide and amino acid filters (nucleotideEquals/aminoAcidEquals, hasMutation/hasAAMutation, insertionContains/aminoAcidInsertionContains, symbolInSet and the mutation profile filters).

Features

• app: add a --version command to the silo binary (8b3146e)
• preprocessing: remove default sequence names from database config (#1386) (b8712ec)
• silo: allow updating of string columns (4d7c561)

[Copilot]

Pull request overview

Adds missing update support for all string-column implementations so SaneQL/Python update_column can reassign plain, indexed, and zstd-compressed string fields (with explicit rejections for phylo-tree and lineage-index backed columns).

Changes:

• Implement update(row_ids, optional<string>) for StringColumn, IndexedStringColumn, and ZstdCompressedStringColumn.
• Extend scalar update dispatch to allow string updates and add targeted rejection errors for phylo/lineage-backed columns.
• Add/extend C++ + Python tests and update Python binding documentation to reflect string update support.

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/silo/storage/column/zstd_compressed_string_column.test.cpp	Adds unit test verifying update overwrites values (and nullability) across chunks.
src/silo/storage/column/zstd_compressed_string_column.h	Exposes update(...) API for zstd-compressed string columns.
src/silo/storage/column/zstd_compressed_string_column.cpp	Implements zstd-compressed string updates + null bitmap maintenance.
src/silo/storage/column/string_column.test.cpp	Adds unit test verifying chunk rebuild behavior and null toggling on update.
src/silo/storage/column/string_column.h	Updates chunk immutability doc and exposes update(...) API for plain string columns.
src/silo/storage/column/string_column.cpp	Implements chunk-rebuild-based updates for plain string columns.
src/silo/storage/column/indexed_string_column.test.cpp	Adds unit test ensuring updates keep inverted index consistent and handle null transitions.
src/silo/storage/column/indexed_string_column.h	Exposes update(...) API for indexed string columns.
src/silo/storage/column/indexed_string_column.cpp	Implements indexed-string updates while maintaining dictionary + inverted index + null bitmap.
src/silo/query_engine/scalar_column_update.cpp	Enables scalar updates for string types and adds explicit rejection messages for phylo/lineage-backed columns.
src/silo/database.test.cpp	Adds DB-level coverage for updating indexed string columns (including null and new dictionary values).
python/tests/test_database.py	Adds end-to-end Python tests for updating a plain string column via bindings.
python/silodb/database.pyx	Updates docstring to include quoted string literals + supported column types/rejections.
documentation/python_bindings.md	Updates user docs for update_column to include string updates and restrictions.

[fengelniederhammer]

LGTM 👍